3a1f: Difference between revisions

Latest revision as of 13:59, 13 March 2024

The crystal structure of NADPH binding domain of gp91(phox)

Structural highlights

3a1f is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	NI
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

CY24B_HUMAN Defects in CYBB are a cause of granulomatous disease,chronic, X-linked (CGD) [MIM:306400. A disorder characterized by the inability of neutrophils and phagocytes to kill microbes that they have ingested. Patients suffer from life-threatening bacterial/fungal infections.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13] ^[14] ^[15] ^[16] ^[17] ^[18] ^[19] ^[20] Defects in CYBB are a cause of mycobacteriosis atypical X-linked type 2 (AMCBX2) [MIM:300645. A rare condition characterized by predisposition to illness caused by moderately virulent mycobacterial species, such as Bacillus Calmette-Guerin (BCG) vaccine and environmental non-tuberculous mycobacteria, and by the more virulent Mycobacterium tuberculosis. Other microorganisms rarely cause severe clinical disease in individuals with susceptibility to mycobacterial infections.^[21]

Function

CY24B_HUMAN Critical component of the membrane-bound oxidase of phagocytes that generates superoxide. It is the terminal component of a respiratory chain that transfers single electrons from cytoplasmic NADPH across the plasma membrane to molecular oxygen on the exterior. Also functions as a voltage-gated proton channel that mediates the H(+) currents of resting phagocytes. It participates in the regulation of cellular pH and is blocked by zinc.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

↑ Jirapongsananuruk O, Niemela JE, Malech HL, Fleisher TA. CYBB mutation analysis in X-linked chronic granulomatous disease. Clin Immunol. 2002 Jul;104(1):73-6. PMID:12139950
↑ Dinauer MC, Curnutte JT, Rosen H, Orkin SH. A missense mutation in the neutrophil cytochrome b heavy chain in cytochrome-positive X-linked chronic granulomatous disease. J Clin Invest. 1989 Dec;84(6):2012-6. PMID:2556453 doi:https://dx.doi.org/10.1172/JCI114393
↑ Bolscher BG, de Boer M, de Klein A, Weening RS, Roos D. Point mutations in the beta-subunit of cytochrome b558 leading to X-linked chronic granulomatous disease. Blood. 1991 Jun 1;77(11):2482-7. PMID:1710153
↑ Ariga T, Sakiyama Y, Tomizawa K, Imajoh-Ohmi S, Kanegasaki S, Matsumoto S. A newly recognized point mutation in the cytochrome b558 heavy chain gene replacing alanine57 by glutamic acid, in a patient with cytochrome b positive X-linked chronic granulomatous disease. Eur J Pediatr. 1993 Jun;152(6):469-72. PMID:8101486
↑ Ariga T, Sakiyama Y, Matsumoto S. Two novel point mutations in the cytochrome b 558 heavy chain gene, detected in two Japanese patients with X-linked chronic granulomatous disease. Hum Genet. 1994 Oct;94(4):441. PMID:7927345
↑ Leusen JH, de Boer M, Bolscher BG, Hilarius PM, Weening RS, Ochs HD, Roos D, Verhoeven AJ. A point mutation in gp91-phox of cytochrome b558 of the human NADPH oxidase leading to defective translocation of the cytosolic proteins p47-phox and p67-phox. J Clin Invest. 1994 May;93(5):2120-6. PMID:8182143 doi:https://dx.doi.org/10.1172/JCI117207
↑ Hui YF, Chan SY, Lau YL. Identification of mutations in seven Chinese patients with X-linked chronic granulomatous disease. Blood. 1996 Nov 15;88(10):4021-8. PMID:8916969
↑ Jendrossek V, Ritzel A, Neubauer B, Heyden S, Gahr M. An in-frame triplet deletion within the gp91-phox gene in an adult X-linked chronic granulomatous disease patient with residual NADPH-oxidase activity. Eur J Haematol. 1997 Feb;58(2):78-85. PMID:9111587
↑ Rae J, Newburger PE, Dinauer MC, Noack D, Hopkins PJ, Kuruto R, Curnutte JT. X-Linked chronic granulomatous disease: mutations in the CYBB gene encoding the gp91-phox component of respiratory-burst oxidase. Am J Hum Genet. 1998 Jun;62(6):1320-31. PMID:9585602 doi:10.1086/301874
↑ Tsuda M, Kaneda M, Sakiyama T, Inana I, Owada M, Kiryu C, Shiraishi T, Kakinuma K. A novel mutation at a probable heme-binding ligand in neutrophil cytochrome b558 in atypical X-linked chronic granulomatous disease. Hum Genet. 1998 Oct;103(4):377-81. PMID:9856476
↑ Dusi S, Nadalini KA, Donini M, Zentilin L, Wientjes FB, Roos D, Giacca M, Rossi F. Nicotinamide-adenine dinucleotide phosphate oxidase assembly and activation in EBV-transformed B lymphoblastoid cell lines of normal and chronic granulomatous disease patients. J Immunol. 1998 Nov 1;161(9):4968-74. PMID:9794433
↑ Ariga T, Furuta H, Cho K, Sakiyama Y. Genetic analysis of 13 families with X-linked chronic granulomatous disease reveals a low proportion of sporadic patients and a high proportion of sporadic carriers. Pediatr Res. 1998 Jul;44(1):85-92. PMID:9667376 doi:10.1203/00006450-199807000-00014
↑ Roesler J, Heyden S, Burdelski M, Schafer H, Kreth HW, Lehmann R, Paul D, Marzahn J, Gahr M, Rosen-Wolff A. Uncommon missense and splice mutations and resulting biochemical phenotypes in German patients with X-linked chronic granulomatous disease. Exp Hematol. 1999 Mar;27(3):505-11. PMID:10089913
↑ Patino PJ, Perez JE, Lopez JA, Condino-Neto A, Grumach AS, Botero JH, Curnutte JT, Garcia de Olarte D. Molecular analysis of chronic granulomatous disease caused by defects in gp91-phox. Hum Mutat. 1999;13(1):29-37. PMID:9888386 doi:<29::AID-HUMU3>3.0.CO;2-X 10.1002/(SICI)1098-1004(1999)13:1<29::AID-HUMU3>3.0.CO;2-X
↑ Ishibashi F, Nunoi H, Endo F, Matsuda I, Kanegasaki S. Statistical and mutational analysis of chronic granulomatous disease in Japan with special reference to gp91-phox and p22-phox deficiency. Hum Genet. 2000 May;106(5):473-81. PMID:10914676
↑ Gerard B, El Benna J, Alcain F, Gougerot-Pocidalo MA, Grandchamp B, Chollet-Martin S. Characterization of 11 novel mutations in the X-linked chronic granulomatous disease (CYBB gene). Hum Mutat. 2001 Aug;18(2):163. PMID:11462241 doi:10.1002/humu.1166
↑ Stasia MJ, Lardy B, Maturana A, Rousseau P, Martel C, Bordigoni P, Demaurex N, Morel F. Molecular and functional characterization of a new X-linked chronic granulomatous disease variant (X91+) case with a double missense mutation in the cytosolic gp91phox C-terminal tail. Biochim Biophys Acta. 2002 Apr 24;1586(3):316-30. PMID:11997083
↑ Bionda C, Li XJ, van Bruggen R, Eppink M, Roos D, Morel F, Stasia MJ. Functional analysis of two-amino acid substitutions in gp91 phox in a patient with X-linked flavocytochrome b558-positive chronic granulomatous disease by means of transgenic PLB-985 cells. Hum Genet. 2004 Oct;115(5):418-27. Epub 2004 Aug 24. PMID:15338276 doi:10.1007/s00439-004-1173-z
↑ Bakri FG, Martel C, Khuri-Bulos N, Mahafzah A, El-Khateeb MS, Al-Wahadneh AM, Hayajneh WA, Hamamy HA, Maquet E, Molin M, Stasia MJ. First report of clinical, functional, and molecular investigation of chronic granulomatous disease in nine Jordanian families. J Clin Immunol. 2009 Mar;29(2):215-30. doi: 10.1007/s10875-008-9243-y. Epub 2008 , Sep 5. PMID:18773283 doi:10.1007/s10875-008-9243-y
↑ Boog B, Quach A, Costabile M, Smart J, Quinn P, Singh H, Gold M, Booker G, Choo S, Hii CS, Ferrante A. Identification and functional characterization of two novel mutations in the alpha-helical loop (residues 484-503) of CYBB/gp91(phox) resulting in the rare X91(+) variant of chronic granulomatous disease. Hum Mutat. 2012 Mar;33(3):471-5. doi: 10.1002/humu.22003. Epub 2012 Jan 3. PMID:22125116 doi:10.1002/humu.22003
↑ Bustamante J, Arias AA, Vogt G, Picard C, Galicia LB, Prando C, Grant AV, Marchal CC, Hubeau M, Chapgier A, de Beaucoudrey L, Puel A, Feinberg J, Valinetz E, Janniere L, Besse C, Boland A, Brisseau JM, Blanche S, Lortholary O, Fieschi C, Emile JF, Boisson-Dupuis S, Al-Muhsen S, Woda B, Newburger PE, Condino-Neto A, Dinauer MC, Abel L, Casanova JL. Germline CYBB mutations that selectively affect macrophages in kindreds with X-linked predisposition to tuberculous mycobacterial disease. Nat Immunol. 2011 Mar;12(3):213-21. doi: 10.1038/ni.1992. Epub 2011 Jan 30. PMID:21278736 doi:10.1038/ni.1992

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Jirapongsananuruk O, Niemela JE, Malech HL, Fleisher TA. CYBB mutation analysis in X-linked chronic granulomatous disease. Clin Immunol. 2002 Jul;104(1):73-6. PMID:12139950

[2] Dinauer MC, Curnutte JT, Rosen H, Orkin SH. A missense mutation in the neutrophil cytochrome b heavy chain in cytochrome-positive X-linked chronic granulomatous disease. J Clin Invest. 1989 Dec;84(6):2012-6. PMID:2556453 doi:https://dx.doi.org/10.1172/JCI114393

[3] Bolscher BG, de Boer M, de Klein A, Weening RS, Roos D. Point mutations in the beta-subunit of cytochrome b558 leading to X-linked chronic granulomatous disease. Blood. 1991 Jun 1;77(11):2482-7. PMID:1710153

[4] Ariga T, Sakiyama Y, Tomizawa K, Imajoh-Ohmi S, Kanegasaki S, Matsumoto S. A newly recognized point mutation in the cytochrome b558 heavy chain gene replacing alanine57 by glutamic acid, in a patient with cytochrome b positive X-linked chronic granulomatous disease. Eur J Pediatr. 1993 Jun;152(6):469-72. PMID:8101486

[5] Ariga T, Sakiyama Y, Matsumoto S. Two novel point mutations in the cytochrome b 558 heavy chain gene, detected in two Japanese patients with X-linked chronic granulomatous disease. Hum Genet. 1994 Oct;94(4):441. PMID:7927345

[6] Leusen JH, de Boer M, Bolscher BG, Hilarius PM, Weening RS, Ochs HD, Roos D, Verhoeven AJ. A point mutation in gp91-phox of cytochrome b558 of the human NADPH oxidase leading to defective translocation of the cytosolic proteins p47-phox and p67-phox. J Clin Invest. 1994 May;93(5):2120-6. PMID:8182143 doi:https://dx.doi.org/10.1172/JCI117207

[7] Hui YF, Chan SY, Lau YL. Identification of mutations in seven Chinese patients with X-linked chronic granulomatous disease. Blood. 1996 Nov 15;88(10):4021-8. PMID:8916969

[8] Jendrossek V, Ritzel A, Neubauer B, Heyden S, Gahr M. An in-frame triplet deletion within the gp91-phox gene in an adult X-linked chronic granulomatous disease patient with residual NADPH-oxidase activity. Eur J Haematol. 1997 Feb;58(2):78-85. PMID:9111587

[9] Rae J, Newburger PE, Dinauer MC, Noack D, Hopkins PJ, Kuruto R, Curnutte JT. X-Linked chronic granulomatous disease: mutations in the CYBB gene encoding the gp91-phox component of respiratory-burst oxidase. Am J Hum Genet. 1998 Jun;62(6):1320-31. PMID:9585602 doi:10.1086/301874

[10] Tsuda M, Kaneda M, Sakiyama T, Inana I, Owada M, Kiryu C, Shiraishi T, Kakinuma K. A novel mutation at a probable heme-binding ligand in neutrophil cytochrome b558 in atypical X-linked chronic granulomatous disease. Hum Genet. 1998 Oct;103(4):377-81. PMID:9856476

[11] Dusi S, Nadalini KA, Donini M, Zentilin L, Wientjes FB, Roos D, Giacca M, Rossi F. Nicotinamide-adenine dinucleotide phosphate oxidase assembly and activation in EBV-transformed B lymphoblastoid cell lines of normal and chronic granulomatous disease patients. J Immunol. 1998 Nov 1;161(9):4968-74. PMID:9794433

[12] Ariga T, Furuta H, Cho K, Sakiyama Y. Genetic analysis of 13 families with X-linked chronic granulomatous disease reveals a low proportion of sporadic patients and a high proportion of sporadic carriers. Pediatr Res. 1998 Jul;44(1):85-92. PMID:9667376 doi:10.1203/00006450-199807000-00014

[13] Roesler J, Heyden S, Burdelski M, Schafer H, Kreth HW, Lehmann R, Paul D, Marzahn J, Gahr M, Rosen-Wolff A. Uncommon missense and splice mutations and resulting biochemical phenotypes in German patients with X-linked chronic granulomatous disease. Exp Hematol. 1999 Mar;27(3):505-11. PMID:10089913

[14] Patino PJ, Perez JE, Lopez JA, Condino-Neto A, Grumach AS, Botero JH, Curnutte JT, Garcia de Olarte D. Molecular analysis of chronic granulomatous disease caused by defects in gp91-phox. Hum Mutat. 1999;13(1):29-37. PMID:9888386 doi:<29::AID-HUMU3>3.0.CO;2-X 10.1002/(SICI)1098-1004(1999)13:1<29::AID-HUMU3>3.0.CO;2-X

[15] Ishibashi F, Nunoi H, Endo F, Matsuda I, Kanegasaki S. Statistical and mutational analysis of chronic granulomatous disease in Japan with special reference to gp91-phox and p22-phox deficiency. Hum Genet. 2000 May;106(5):473-81. PMID:10914676

[16] Gerard B, El Benna J, Alcain F, Gougerot-Pocidalo MA, Grandchamp B, Chollet-Martin S. Characterization of 11 novel mutations in the X-linked chronic granulomatous disease (CYBB gene). Hum Mutat. 2001 Aug;18(2):163. PMID:11462241 doi:10.1002/humu.1166

[17] Stasia MJ, Lardy B, Maturana A, Rousseau P, Martel C, Bordigoni P, Demaurex N, Morel F. Molecular and functional characterization of a new X-linked chronic granulomatous disease variant (X91+) case with a double missense mutation in the cytosolic gp91phox C-terminal tail. Biochim Biophys Acta. 2002 Apr 24;1586(3):316-30. PMID:11997083

[18] Bionda C, Li XJ, van Bruggen R, Eppink M, Roos D, Morel F, Stasia MJ. Functional analysis of two-amino acid substitutions in gp91 phox in a patient with X-linked flavocytochrome b558-positive chronic granulomatous disease by means of transgenic PLB-985 cells. Hum Genet. 2004 Oct;115(5):418-27. Epub 2004 Aug 24. PMID:15338276 doi:10.1007/s00439-004-1173-z

[19] Bakri FG, Martel C, Khuri-Bulos N, Mahafzah A, El-Khateeb MS, Al-Wahadneh AM, Hayajneh WA, Hamamy HA, Maquet E, Molin M, Stasia MJ. First report of clinical, functional, and molecular investigation of chronic granulomatous disease in nine Jordanian families. J Clin Immunol. 2009 Mar;29(2):215-30. doi: 10.1007/s10875-008-9243-y. Epub 2008 , Sep 5. PMID:18773283 doi:10.1007/s10875-008-9243-y

[20] Boog B, Quach A, Costabile M, Smart J, Quinn P, Singh H, Gold M, Booker G, Choo S, Hii CS, Ferrante A. Identification and functional characterization of two novel mutations in the alpha-helical loop (residues 484-503) of CYBB/gp91(phox) resulting in the rare X91(+) variant of chronic granulomatous disease. Hum Mutat. 2012 Mar;33(3):471-5. doi: 10.1002/humu.22003. Epub 2012 Jan 3. PMID:22125116 doi:10.1002/humu.22003

[21] Bustamante J, Arias AA, Vogt G, Picard C, Galicia LB, Prando C, Grant AV, Marchal CC, Hubeau M, Chapgier A, de Beaucoudrey L, Puel A, Feinberg J, Valinetz E, Janniere L, Besse C, Boland A, Brisseau JM, Blanche S, Lortholary O, Fieschi C, Emile JF, Boisson-Dupuis S, Al-Muhsen S, Woda B, Newburger PE, Condino-Neto A, Dinauer MC, Abel L, Casanova JL. Germline CYBB mutations that selectively affect macrophages in kindreds with X-linked predisposition to tuberculous mycobacterial disease. Nat Immunol. 2011 Mar;12(3):213-21. doi: 10.1038/ni.1992. Epub 2011 Jan 30. PMID:21278736 doi:10.1038/ni.1992

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 3a1f is ON HOLD  until Paper Publication
+==The crystal structure of NADPH binding domain of gp91(phox)==
+<StructureSection load='3a1f' size='340' side='right'caption='[[3a1f]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3a1f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A1F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A1F FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3a1f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a1f OCA], [https://pdbe.org/3a1f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a1f RCSB], [https://www.ebi.ac.uk/pdbsum/3a1f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a1f ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/CY24B_HUMAN CY24B_HUMAN] Defects in CYBB are a cause of granulomatous disease,chronic, X-linked (CGD) [MIM:[https://omim.org/entry/306400 306400]. A disorder characterized by the inability of neutrophils and phagocytes to kill microbes that they have ingested. Patients suffer from life-threatening bacterial/fungal infections.<ref>PMID:12139950</ref> <ref>PMID:2556453</ref> <ref>PMID:1710153</ref> <ref>PMID:8101486</ref> <ref>PMID:7927345</ref> <ref>PMID:8182143</ref> <ref>PMID:8916969</ref> <ref>PMID:9111587</ref> <ref>PMID:9585602</ref> <ref>PMID:9856476</ref> <ref>PMID:9794433</ref> <ref>PMID:9667376</ref> <ref>PMID:10089913</ref> <ref>PMID:9888386</ref> <ref>PMID:10914676</ref> <ref>PMID:11462241</ref> <ref>PMID:11997083</ref> <ref>PMID:15338276</ref> <ref>PMID:18773283</ref> <ref>PMID:22125116</ref>   Defects in CYBB are a cause of mycobacteriosis atypical X-linked type 2 (AMCBX2) [MIM:[https://omim.org/entry/300645 300645]. A rare condition characterized by predisposition to illness caused by moderately virulent mycobacterial species, such as Bacillus Calmette-Guerin (BCG) vaccine and environmental non-tuberculous mycobacteria, and by the more virulent Mycobacterium tuberculosis. Other microorganisms rarely cause severe clinical disease in individuals with susceptibility to mycobacterial infections.<ref>PMID:21278736</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/CY24B_HUMAN CY24B_HUMAN] Critical component of the membrane-bound oxidase of phagocytes that generates superoxide. It is the terminal component of a respiratory chain that transfers single electrons from cytoplasmic NADPH across the plasma membrane to molecular oxygen on the exterior. Also functions as a voltage-gated proton channel that mediates the H(+) currents of resting phagocytes. It participates in the regulation of cellular pH and is blocked by zinc.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a1/3a1f_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3a1f ConSurf].
+<div style="clear:both"></div>
-Authors: Honbou, K., Noda, N.N., Sumimoto, H., Inagaki, F.
+==See Also==
+*[[NADPH oxidase 3D structures|NADPH oxidase 3D structures]]
-Description: The crystal structure of NADPH binding domain of gp91(phox)
+== References ==
+<references/>
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 22 11:04:10 2009''
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Honbou K]]

3a1f: Difference between revisions

Latest revision as of 13:59, 13 March 2024

The crystal structure of NADPH binding domain of gp91(phox)

Structural highlights

Disease

Function

Evolutionary Conservation

See Also

References

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Proteopedia Page Contributors and Editors (what is this?)

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